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Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein Networks

Protein Networks

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Organization

Protein Organization

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Updated: May 2, 2026

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

RNA-protein interactions: an overview.

Angela Re¹, Tejal Joshi, Eleonora Kulberkyte

¹University of Trento, Mattarello, Italy.

Methods in Molecular Biology (Clifton, N.J.)

|March 19, 2014

Summary

This summary is machine-generated.

RNA binding proteins (RBPs) regulate gene expression by interacting with RNA. This chapter explores protein-RNA recognition, experimental technologies, and computational tools for studying these interactions and binding sites.

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Area of Science:

Molecular Biology
Bioinformatics
Genetics

Background:

RNA binding proteins (RBPs) are crucial regulators of gene expression.
RBPs control multiple steps of RNA processing, impacting cellular functions.
Understanding RBP-RNA interactions is vital for deciphering gene regulation mechanisms.

Purpose of the Study:

To review protein-RNA recognition modes employed by RBPs.
To present methodologies for studying RBP-RNA interactions, both in vitro and in vivo.
To introduce computational tools for predicting RNA binding sites.

Main Methods:

Discussion of established and advanced experimental technologies for RBP-RNA interaction analysis.
Overview of computational frameworks (unsupervised and supervised) for RNA binding site prediction.
Comparison of protein-RNA and protein-DNA binding site prediction algorithms.

Main Results:

Detailed explanation of diverse protein-RNA recognition strategies.
Presentation of resources for experimentally validated protein-RNA interactions.
Analysis of computational tools, highlighting their modeling features and frameworks.

Conclusions:

RBPs play a central role in gene expression regulation through specific RNA binding modes.
A combination of experimental and computational approaches is essential for comprehensive RBP-RNA interaction studies.
Novel computational methods are being developed to accurately predict RNA binding sites, considering unique RNA features.